Although advances in antiretroviral therapy, in particular Highly Active Antiretroviral Treatment (HAART) multi-drug regimens, have greatly aided the management of HIV infected patients, treatments cannot permanently eliminate HIV and long-lasting HIV reservoirs persist, primarily in lymphoid tissue. Developing new therapies directed against these reservoirs will require analytical methods that can detect low levels of virus and identify the types of cells harboring residual virus. Rare cell detection is currently a tedious procedure due to the time needed to analyze large numbers of cells. Using fluorescence in situ hybridization and automated image analysis, this SBIR aims to develop a high throughput method for quantifying HIV infected cells present in low frequency. This assay will facilitate rapid diagnosis of HIV infection and development of treatments for HIV infection.